User: user230613

gravatar for user230613
user230613250
Reputation:
250
Status:
Trusted
Location:
Europe
Last seen:
1 week, 4 days ago
Joined:
3 years, 1 month ago
Email:
i********@hotmail.com

Posts by user230613

<prev • 59 results • page 1 of 6 • next >
0
votes
2
answers
787
views
2
answers
Comment: C: TPM VS FPKM VS TMM and K-mer specific expression quantification
... Hi Rob. Could you guide me a bit? If I want to find the expression of a given kmer (10nt) that is common between two transcripts, should I add the TPMs of both transcripts? ...
written 5 weeks ago by user230613250
3
votes
1
answer
186
views
1
answer
GATK; Variant calling RNA-Seq best practices: bam processing steps
... Hi folks, I have been looking for the best approach for call the variants in RNA-Seq data. GATK proposes the following workflow: > 1) Map the reads using STAR. > > 2) Remove duplicates > > 3) Split N Trim > > 4) Indel realignment > > 5) Base recalibration > & ...
gatk variant_calling rna-seq written 8 weeks ago by user230613250 • updated 8 weeks ago by andrew.j.skelton734.1k
0
votes
2
answers
259
views
2
answers
Comment: C: Specific sequence abundance using RNA-Seq
... @Brian, I want to measure the expression of that sequence using RNA-Seq data, I don't want to extract the Kmer sequence from my reads. ...
written 4 months ago by user230613250
3
votes
2
answers
259
views
2
answers
Specific sequence abundance using RNA-Seq
... Hi, I would like to measure the expression, the abundance, of a given sequence, a specific 9-mer. I have `RNA-Seq` data. I know that the 9-mer is not unique in the genome, is not private of a specific gene. It is present in more than one isoform of gene A and also is present in gene B. How can I ge ...
expression rna-seq written 5 months ago by user230613250 • updated 5 months ago by Brian Bushnell14k
0
votes
7
answers
13k
views
7
answers
Comment: C: What Ngs Read Simulators Are Available For Paired-End Data?
... Thank you for the fast answer. I'll try the bedtools pre-step. Another issue.. I've realised that in PE mode, the names of the output reads in the two files are not paired, is there any option for this? ...
written 5 months ago by user230613250
0
votes
7
answers
13k
views
7
answers
Comment: C: What Ngs Read Simulators Are Available For Paired-End Data?
... Hi Brian! Is it possible to generate reads in specific intervals? WES-like read simulation? ...
written 5 months ago by user230613250
0
votes
1
answer
215
views
1
answers
Comment: C: Subset of transcripts - Do I need to re-scale the TPM values?
... Mmmm.. that's true, but I'm not interested in the non-coding transcripts at all. That's why I have posted a second question "Is there a difference between this approach or running Kallisto only on those coding transcripts?", because if you use only coding set of transcripts when running kallisto, th ...
written 5 months ago by user230613250
3
votes
1
answer
215
views
1
answer
Subset of transcripts - Do I need to re-scale the TPM values?
... Hi! Apologies in advance if this question is very basic =) I have run `Kallisto` using the full human transcriptome dataset `GRCh37-75`. This dataset includes both coding and non-coding transcripts, obviously. I would like to further analyse the coding ones. Since the `TPM` measurement take into a ...
tpm kallisto rna-seq written 5 months ago by user230613250
7
votes
2
answers
787
views
2
answers
TPM VS FPKM VS TMM and K-mer specific expression quantification
... Hi Biostar's! I'm trying to find the best approach to fill my goal. I would like to measure the expression of specific set of kmers - 10 aa long peptide sequences across different samples. I have RNA-Seq data for each sample. I'm planing to use alignment-independent methods such as `Kallisto` or `S ...
kmer rna-seq written 5 months ago by user230613250 • updated 3 months ago by Rob2.2k
0
votes
2
answers
568
views
2
answers
Comment: C: kallisto: strand-specific and fragment length calculation
... Sorry, I have another question, "fragment-length" is not the same as read length, is it? I mean, it can't be inferred using input SE fastq files ...
written 6 months ago by user230613250

Latest awards to user230613

Popular Question 4 weeks ago, created a question with more than 1,000 views. For promoter position estimation
Popular Question 4 months ago, created a question with more than 1,000 views. For promoter position estimation
Popular Question 4 months ago, created a question with more than 1,000 views. For CIRCOS plot with Chip-Seq Data
Popular Question 6 months ago, created a question with more than 1,000 views. For Intersect multiple bed and keep all fields
Student 6 months ago, asked a question with at least 3 up-votes. For Extract reads within given region, and their mates
Popular Question 10 months ago, created a question with more than 1,000 views. For Trinity strand specific: RF or FR
Popular Question 12 months ago, created a question with more than 1,000 views. For Trinity strand specific: RF or FR
Popular Question 12 months ago, created a question with more than 1,000 views. For Intersect multiple bed and keep all fields
Popular Question 17 months ago, created a question with more than 1,000 views. For Trinity strand specific: RF or FR
Popular Question 17 months ago, created a question with more than 1,000 views. For Extract sequence number "X" from multifasta file
Popular Question 17 months ago, created a question with more than 1,000 views. For Extract reads within given region, and their mates
Supporter 2.6 years ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 615 users visited in the last hour